I would also like to understand what is that exactly you want to achieve as I think, agreeing with Lorys, that having a history of my last key-ins is very handy.
One way of doing this quite quickly, which is not that different from Conor's suggestion but maybe a bit quicker would be to create a second shortcut with the "-restoredefaultsquiet" command line switch and to double click on this whenever you want to delete the key-in history: bear in mind that his will reset Microstation to factory defaults (as basically does deleting the upf) and also clean your temp files.
Here is an article on how to do the above, just do it on a copy of Microstation shortcut called "Reset MicroStation" or something similar.
Restore MicroStation to Factory defaults
Bentley Systems Inc.